[phenixbb] ADP high variance
pafonine at lbl.gov
Thu Mar 20 07:43:58 PDT 2008
Carsten is right, phenix.refine uses a different approach. However,
changing the wxu_scale should visibly change the ADP variances.
- are you using TLS?
- what is the exact command you run?
- if your PDB file has segment identifiers, are they all consistent (no
Normally, changing the wxu_scale has to change the ADP variances. If it
does not change then something is not right somewhere. I need some more
information to tell you exactly what's happening. If you want me to
debug it some more, I'm happy to do so but I will need to reproduce this
problem on myself on computer (meaning I need the model and data).
Daniel Frey wrote:
> I have a good data set to 1.8 A and refined it with the actual version
> of phenix, including annealing and isotropic bfactors. Checking the B
> factor variance in coot revealed high differences in about 50% of the
> residues. Most of them are at the surface, but still there are
> residues like phenylalanines and valines within the core where the
> bfactors jump from 25 to 50 from one carbon atom to the other.
> Changing wu and wxu_scale did not improve the results. A quick check
> with refmac improved the results, so i guess I am missing the right
> restraints for phenix. Which parameters should be changed to improve
> the bfactor variance in phenix?
> Thanks for your help
> Daniel Frey
> Department of Biochmistry
> University of Zurich
> Winterthurerstrass 190
> 8057 Zurich
> freyd at bioc.unizh.ch
> Tel: +41446355558
> phenixbb mailing list
> phenixbb at phenix-online.org
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